Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.

ABSTRACT:

Background

Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence.

Methods

The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalp

SUBMITTER: Konig G 

PROVIDER: S-EPMC4339525 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature